Clock synchronization provides a common time reference for different nodes in the wireless sensor networks to deal with distributed tasks. The wireless sensor networks require accurate clock synchronization to keep the consistence and coordination of data among nodes. However, the unpredictability of message delays in the synchronization process may affect the synchronization accuracy significantly. To eliminate the impact of delay fluctuation, the clock synchronization model is formulated, which considers the influence of delays with Gaussian distribution in the synchronization process. And a Kalman based delay estimation algorithm on distributed clock synchronization is proposed, which can effectively deal with the influence of delays. This algorithm utilizes one-way message exchange mechanism, and all parameters could be updated independently in one node. In addition, the calculated global time is considered as a reference to update the clock offset. In this way, the synchronization accuracy is improved. The MATLAB simulation and the nRF52832 experiment testbed with 5 nodes indicate that this algorithm restricts the synchronization error into 10 μs under microsecond delays. Compared with other algorithms, this method could achieve better synchronization accuracy and performance.